Antigen

Antigen Class

TFs and others

Antigen

Nfil3

Cell type

Cell type Class

Liver

Cell type

Liver

MeSH Description

A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Sample

source_name

E4BP4 TG - E4BP4

strain

C57BL/6

age

8 week old

Sex

male

genotype/variation

liver-specific E4BP4 transgenic

tissue

liver

chip antibody

E4BP4 (sc-28203, Santa Cruz Biotechnology)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

After cervical dislocation, mouse liver was perfused with a buffer containing Hanks' balanced salt solution, and cross-inked for 30 minutes with 2mM DSG and for 10 minutes with 1% formaldehyde by perfusion, followed by frozen at -80C. Then, Liver was homogenated by gentleMACS Dissociators. Nuclei were isolated in buffer containing 1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.0, and protease inhibitors and sonicated using a Diagenode Bioruptor to shear chromatin to 200-1000bp fragments. Protein-DNA complexes were incubated with antibodies against two kinds of E4BP4 (sc-28203, Santa Cruz Biotechnology)and immunoprecipitated with IgG paramagnetic beads (Invitrogen). Eluted chromatin was isolated using MinElute PCR purification columns (Qiagen). Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer's instructions. Library concentrations were assessed by both a Bioanalyzer (Agilent) and NEBNext Library Quant Kit for Illumina (New England Biolabs).

Sequencing Platform

instrument_model

NextSeq 550

mm10

Number of total reads

31448578

Reads aligned (%)

94.4

Duplicates removed (%)

21.8

Number of peaks

335 (qval < 1E-05)

mm9

Number of total reads

31448578

Reads aligned (%)

94.2

Duplicates removed (%)

21.9

Number of peaks

349 (qval < 1E-05)